On 19/09/2011 9:42 AM, Sweta Iyer wrote:
Hi,
I embedded my protein of interest into a DMPC membrane by the g_membed
tool with the following command:
g membed -f input.tpr -p system.top -n index.ndx -xyinit 0.1 -xyend
1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100
I then energy minimized the resultant structure for 1 ns before the
position restraint dynamics and the productive run.
My structure looks fine after the em. However, when I do the PR and
look at the structure it looks weird in that half of the protein is
hanging out of the membrane and there seems to be a patch of water
molecules that seem to have entered the membrane.
I have no clue what must be possibly going wrong here. Should I have
equilibrated the system for longer than 1ns or is it something wrong
with the membrane insertion.
Sounds like the advice here might be useful.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark
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